Networking:
Reduntant 1Gbps fiber optic - Internet Access |
10Gbps Ethernet Core Switching (Juniper Ex45xx/42xx stacks & EX33xx VCP) |
40Gb Infiniband QDR HPC network and/or 10GbE |
10Gb LAN uplink to server room |
Clusters:
64bit Computing Cluster of approx. 35 48&64 core AMD nodes + HTS & big memory nodes (approx. 1750 cores, 13.5 TFLOPs), 3,7TB RAM, Infiniband QDR Interconnect, 10GbE, Ubuntu 16.04 & 10.04, OGE 6.2u7 |
64bit Virtualization Cluster Pool with pool, networking & storage redundancy, approx. 2x768G RAM, 10Gb iSCSI, FC8G, XenServer 7.0, approx 12TB incl. SSD pools |
Storage systems:
500 TB (0,5 PB) storage on Isilon Dell EMC Isilon NL410 nodes (5x) - incl. zoning, snapshots & ACL - accessible with NFS & Windows SMB |
Approximately 200 TB of varied (cut to fit) storage incl. NL-SAS, SAS, SSD, SATA & varuious interfaces for interpoerability (FC, IB, 10GbE, SAS) |
Servers:
(list is currently being updated)
Workstations:
Mostly Core i5, Core i7 or Xeon-bases motherboards with dedicated NVidia GPUs,
(list is currently being updated)
Laptops:
(this list is currently being updated)
Other:
Digital Projector S40, 3M, USA |
Kyocera C2126MFP |
COMPUTER SOFTWARE:
OS:
Production servers: Ubuntu LTS, Debian Stable |
Testing: Gentoo/Slackware/Ubuntu Linux, MS Windows 2003 |
Workstations: Ubuntu, Debian, MacOS, MS Windows Terminal Services |
Molecular Modeling:
AMBER, University of California, San Francisco, USA |
CABS, Warsaw University, Warsaw, Poland |
CHARMM, Harvard University, Cambridge, USA |
CNS, Yale University, New Haven, USA |
HYPERCHEM 7.1, Hypercube, Inc., Gainesville, USA |
INSIGHT II, Catalyst, Accelrys Software Inc., USA |
MODELLER 9v1, University of California, San Francisco, USA |
MOLSCRIPT 2.1.2, Avatar Software AB, Sweden |
MC-SYM 3.3.2. UniversitĂŠ de MontrĂŠal, Canada |
NAMD 2.6, Beckman Institute, USA |
REFINER, Warsaw University, Warsaw, Poland |
ROSETTA, University of Washington, Seattle, USA |
SCULPT 3.0, Elsevier MDL, San Ramon, USA |
SCWRL 3.0, Fox Chase Cancer Center, Philadelphia, USA |
SYBYL 7.3, Tripos, USA |
UNRES, University of Gdansk, Gdansk, Poladnd |
ERNA3D, PENTAFOLIUM-SOFT, Rosengarten, Germany |
Docking:
AUTODOCK, The Scripps Research Institute, La Jolla, USA |
BIGGER, Universidade Nova de Lisboa, Caparica, Portugal |
DOCK, University of California, San Francisco, USA |
GRAMM, University of Kansas, Lawrence, USA |
HADDOCK, Utrecht University, the Netherlands |
RDOCK, Boston University, Boston, USA |
SURFLEX, BioPharmics LLC, USA |
ZDOCK, Boston University, Boston, USA |
Sequence Analysis:
Clone Manager 7, Scientific & Educational Software, USA |
CLANS & HHpred, Max Planck Institute of Developmental Biology, Tuebingen, Germany |
NCBI Toolkit 6.1, NCBI, Bethesda, USA |
Statistica 7 & Data Mining, StatSoft., USA |
Office:
ENDNOTE, ISI ResearchSoft, Berkeley, USA |
MS Office XP, Microsoft Corp., USA |
VMware Workstation 5, Mware, Inc., USA |
CrossOver Office 4.2, CodeWeavers, USA |
MS Office 2010, Microsoft Corp., USA |
MS Windows 7 Pro, Microsoft Corp., USA |
WET LAB HARDWARE:
Protein and nucleic acid biochemistry:
CD Spectropolarimeter JASCO J-810, Jasco, Japan |
ASM-800 DNA Synthesizer, Biosset Ltd., Russia |
OPS-201 Oligonucleotide Purification System, Biosset Ltd., Russia |
ABI Prism 310 Genetic Analyzer, Capillary DNA Sequencer, Applied Biosystems, USA |
Minicycler, MJ Reasearch, USA |
MJ Mini Personal Thermal Cycler, Bio-Rad Laboratories, Inc., USA |
C1000 Thermal Cycler Chassis, Bio-Rad Laboratories, Inc., USA |
Immersion Circulator 7312, PolyScience, USA |
Fraction collector, Brandel, USA |
Tensor 27, FTIR Spectrometer, Bruker, German |
Chromatographic systems:
2x BioLogic LP, Bio-Rad Laboratories, Inc., USA |
AKTA Purifier, GE Healthcare, USA |
Avant, GE Healthcare, USA |
HPLC, Waters, USA |
Cell cultures:
2x Incubated orbital shaker Unitron - plus, Infors AG, Switzerland |
Electrophoresis:
DNA - horizontal gel electrophoresis systems: |
2x SUBDNA, Kucharczyk TE, Poland |
SUBMINI, Kucharczyk TE, Poland |
SHU13, Sigma-Aldrich, USA |
SHU6, Sigma-Aldrich, USA |
Protein - vertical gel electrophoresis systems:
3x PROTEAN II, Bio-Rad Laboratories, Inc., USA, |
MINI PROTEAN tetra electrophoresis system, Bio-Rad Laboratories, Inc., USA, |
MINIPOL 2, Kucharczyk TE, Poland |
2x Vertical Electrophoresis system large scale, C.B.S Scientific, USA |
Power supplies:
2x E844, Consort nv, Belgium |
2x EV232, Consort nv, Belgium |
E132, Consort nv, Belgium |
Protein blotting:
Mini Trans-Blot Cell, Bio-Rad Laboratories, Inc., USA, |
2x Semi-dry blotters SV20-SDB, Sigma-Aldrich, USA |
96 well Dot-Blot Hybridization Manifold, SciePlas Ltd., UK |
Microcentrifuges:
Mikro 20, Hettich, Germany |
5415 D, Eppendorf, Germany |
5804 R, Eppendorf, Germany |
5418, Eppendorf, Germany |
5117R, Eppendorf, Germany |
5810R, Eppendorf, Germany |
Other equipment:
pH 211 Microprocessor pHMeter, Hanna Instruments, USA |
Water Bath (Model WB), Memmert, Germany |
Unimax shaker, Heidolph Instruments GmbH & Co. KG, Germany |
3xThermomixer comfort, Eppendorf, Germany |
Deepfreezer ULT 2186-3, Revco Thermo Electron Corporation, USA |
Micro-Pulser, Bio-Rad Laboratories, Inc., USA |
A CATALOG of other equipment freely available to the Bujnicki lab in IIMCB.